Contacts of the helix formed by residues 273 - 283 (chain B) in PDB entry 5W5T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B ARG* 3.4 36.1 - - + +
27B LEU* 3.4 9.2 - - - +
271B VAL 4.0 0.3 - - - +
272B GLY* 1.3 82.4 - - - +
274B ILE* 1.3 59.8 + - - +
275B ASP* 3.7 8.3 + - - +
276B ALA* 3.1 24.2 + - + +
277B TYR* 2.7 30.0 + - - +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ARG 4.0 7.0 + - - +
27B LEU* 3.7 28.5 - - + +
28B LYS* 3.9 12.8 - - + +
30B LEU* 5.7 3.6 - - + -
273B THR* 1.3 70.8 - - - +
275B ASP* 1.3 56.8 + - - +
277B TYR* 3.5 7.7 - - + +
278B TRP* 2.7 34.5 + - - +
377B VAL* 4.5 8.1 - - + -
402B ARG* 3.7 30.5 - - + -
404B THR* 3.9 22.4 - - + +
408B ILE* 3.9 17.7 - - + -
410B LEU* 3.7 21.1 - - + -
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B THR* 3.4 7.2 + - - +
274B ILE* 1.3 77.6 - - - +
276B ALA* 1.3 51.7 + - - +
278B TRP* 3.6 7.7 - - + +
279B GLN* 2.7 38.3 + - - +
404B THR* 2.7 32.3 + - - +
405B GLU* 5.1 1.2 + - - +
406B SER* 3.7 22.7 + - - -
408B ILE* 3.4 14.1 - - - +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B VAL* 3.7 20.0 - - + +
272B GLY 4.1 2.0 - - - +
273B THR* 3.1 26.0 + - + +
275B ASP* 1.3 76.2 - - - +
277B TYR* 1.3 57.7 + - - +
279B GLN* 3.8 5.5 - - - +
280B ALA* 2.8 33.1 + - - +
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Residues in contact with TYR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 4.2 9.9 - - + -
30B LEU* 3.7 22.2 - - + -
39B VAL* 3.3 24.6 - - + +
40B TYR 2.7 32.3 + - - -
41B PHE* 5.0 3.1 - + + -
47B ILE* 5.4 0.7 - - + -
271B VAL* 3.7 25.3 - - + +
273B THR 2.7 21.2 + - - +
274B ILE* 3.5 8.3 - - + +
276B ALA* 1.3 71.1 - - - +
278B TRP* 1.3 66.2 + - - +
280B ALA* 3.4 1.0 + - - +
281B ASN* 2.8 48.7 + - - -
345B PHE* 4.7 1.4 - - - -
360B VAL* 4.6 3.4 - - + -
362B LEU* 3.6 24.0 - - + +
377B VAL* 3.8 28.5 - - + -
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Residues in contact with TRP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ILE 2.7 21.0 + - - +
275B ASP* 3.7 6.3 - - - +
277B TYR* 1.3 75.1 - - - +
279B GLN* 1.3 106.1 + - - +
281B ASN* 3.3 1.6 + - - +
282B ILE* 2.9 43.5 + - + +
341B ARG* 4.2 9.9 - - - -
358B ASN* 2.9 36.7 + - + -
360B VAL* 3.8 17.3 - - + +
375B ASN* 3.8 22.2 - - - -
376B VAL 3.5 19.8 + - - +
377B VAL* 3.8 17.3 - - + -
406B SER* 5.9 1.8 - - - -
408B ILE* 3.5 32.9 - - + +
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B ASP 2.7 23.9 + - - +
276B ALA* 3.8 6.1 - - - +
278B TRP* 1.3 96.0 - - - +
280B ALA* 1.3 60.7 + - - +
282B ILE* 4.0 11.1 - - - +
283B ASP* 2.9 63.3 + - - +
341B ARG* 4.6 5.3 - - - +
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.8 17.2 - - + -
267B TYR* 4.2 14.8 + - - +
269B ARG* 4.7 15.0 - - + +
271B VAL* 3.6 21.3 - - + -
276B ALA 2.8 20.8 + - - +
277B TYR 4.0 0.9 - - - +
279B GLN* 1.3 74.0 - - - +
281B ASN* 1.3 62.0 + - - +
283B ASP* 3.8 12.7 + - - +
284B LEU* 3.7 15.4 - - - +
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Residues in contact with ASN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.3 16.9 - - - -
42B GLY 2.9 30.0 + - - -
277B TYR* 2.8 53.8 + - - +
280B ALA* 1.3 76.9 - - - +
282B ILE* 1.3 65.3 + - - +
284B LEU* 2.9 24.7 + - - +
285B THR 4.2 0.7 + - - -
343B LEU* 3.3 27.7 - - + +
345B PHE* 4.1 1.6 - - - -
360B VAL* 3.6 20.9 - - + -
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Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B TRP* 2.9 37.0 + - + +
279B GLN* 3.9 19.5 - - - +
281B ASN* 1.3 77.2 - - - +
283B ASP* 1.3 62.8 + - - +
285B THR* 2.7 31.4 + - + +
286B ASP* 4.3 1.7 + - - +
341B ARG* 3.6 50.1 + - + +
342B SER* 4.2 1.1 - - - -
343B LEU* 4.2 8.3 - - + +
358B ASN* 4.1 3.1 - - - -
359B ALA 3.4 31.4 - - - +
360B VAL* 3.6 16.2 - - + -
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Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ARG* 5.2 6.4 + - - -
279B GLN* 2.9 55.1 + - - +
280B ALA* 3.9 9.5 - - - +
281B ASN 3.1 0.4 - - - -
282B ILE* 1.3 77.9 - - - +
284B LEU* 1.3 62.9 + - + +
285B THR 3.0 1.7 + - - -
286B ASP* 3.1 36.4 + - - +
289B PRO* 3.6 8.6 - - - +
290B ASP* 4.4 18.8 - - + +
341B ARG* 4.4 4.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il